Well... I'm not going to say it makes sense, becuase I'm not sure if anybody really thought that deeply about it. But I can imagine that the aliens are somehow a single-gender species. They need to mix with the DNA of another species in order to reproduce. After all, the creatures take on different characteristics based on their hosts. This is also how they're able to survive on the planet which they're used on. The "queen" is not a queen per se. Simply an egg laying male. (Or perhaps they're all female.) So the face huggers are simply the vessel for doing that.
And here's something I NEVER understood about the Alien species, but I needed to watch one of the movies before I said this: What's the point of the facehuggers? Seriously, what are they? They stick to a host and make them pregnant with the actual Alien, then dies? I never understood that. Just because it's a scary and original idea doesn't mean that it can't make sense.